python

About

Python is a dynamic object-oriented scripting language
that can be used for many kinds of software development. It offers
strong support for integration with other languages and tools,
comes with extensive standard libraries, and can be learned in a
few days.

Versions and Availability

▶ Display Softenv Keys for python on all clusters

Machine

Version

Softenv Key

eric

2.6.4

+python-2.6.4-gcc-4.3.2

eric

2.6.4

+python-2.6.4-intel-11.1

eric

2.7.3

+python-2.7.3-gcc-4.3.2

eric

3.1.1

+python-3.1.1-gcc-4.3.2

philip

2.6.4

+python-2.6.4-intel-11.1

philip

2.7.3

+python-2.7.3-gcc-4.3.2

pandora

2.7.3

+python-2.7.3

supermike2

2.7.3

+Python-2.7.3-gcc-4.4.6

▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

▶ Display Module Names for python on all clusters.

Machine

Version

Module

smic

2.7.7-anaconda

python/2.7.7-anaconda

qb2

2.7.7-anaconda

python/2.7.7-anaconda

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business
of setting up their shell environment in the face of potentially
conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules
in their home directory. This file contains module commands to
set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look
something like:

Usage

The Python language can be used like most other scripting
languages. Issuing the command alone, python, starts a
interactive pythonic shell session. If a Python program is
contained in a file command-line execution is
possible:

$ python [options] [-c cmd | -m mod | file | -] [arg [args ...]]

Use python --help for quick help, and see the
documentation in the resource section for language details.

▶ Executable Scripts FAQ?

Executable Scripts

All shells and most interpreters (i.e. Python, Tcl, gawk, R, etc.)
can be used to create executable scripts. This is accomplished through
the magic of the shell #! line, which is a special comment
line. The line, which must be the first line of the script, specifies
the path to the program that can interpret the main contents of the
file, which are command lines the language understands. Once the
script is written, set it executable with chmod. A few examples
should serve to illustrate the general idea.

Executable Bash Script

A simple script to echo out Hello World and do a long ls
listing.

#!/bin/bash
echo "Hello World!"
ls -l

If the above is in a file named hello.sh, it can be made
executable for the user (i.e. see man chmod for other
possibilities) and run with:

$ chmod u+x hello.sh
$ ./hello.sh

Other Scripts

Here are some line usable with other scripting languages. In most
cases, options allowed by the command used can be provided on
the #! line. Note: that the paths should be verified and
not use blindly. In particular command shells tend to reside in
different directories.